Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.
DynaFit – analysis of (bio)chemical kinetics and equilibria.
The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance).
Scaffold Hunter is a tool for the visual analysis of data from the life sciences, aiming at intuitive access to large and complex data sets that offers a variety of views and analysis methods. It originates from drug discovery and has evolved into a reusable open source platform for a wider range of applications.
BioSM is a cheminformatics tool that uses known mammalian biochemical compounds (scaffolds) and graph matching methods to identify biochemical structures in chemical structure space
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
Biochemistry Lab Suite app aims in helping scientists and students working in the field of mass spectrometry based proteomics, metabolomics, biochemistry, biology and chemistry but also aids in general lab work.
Bioinformatics. 2009 Mar 15;25(6):836-7. doi: 10.1093/bioinformatics/btp069. Epub 2009 Feb 25. BISEN: Biochemical Simulation Environment.
Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA.
ECOH is a new method to assign Enzyme Commission numbers using a maximum common substructure algorithm, mutual information and a support vector machine.
Prometheus is a versatile software platform for the storage, management, and analysis of fermentation data. The multi application system allows storing of arbitrary online and offline parameters and supports gene expression studies by including existing applications for microarray and qPCR analysis. The newly developed application Prometheus features data import, runtime chart generation, data statistics, and a versatile data export mechanism. The platform can be accessed using a web browser and exposes many functions as a web service. The complete system is protected by a user management system providing single sign on and fine grained data sharing mechanisms.